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- PDB-2dlf: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI... -

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Entry
Database: PDB / ID: 2dlf
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 6.75
Components
  • PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) (HEAVY CHAIN))
  • PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)-KAPPA (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / FV FRAGMENT / IMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-II region 26-10 / Ig heavy chain V-III region J606
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNakasako, M. / Takahashi, H. / Shimada, I. / Arata, Y.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.
Authors: Nakasako, M. / Takahashi, H. / Shimba, N. / Shimada, I. / Arata, Y.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragment of Anti- ...Title: Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragment of Anti-Dansyl Mouse Monoclonal Antibody
Authors: Takahashi, H. / Tamura, H. / Shimba, N. / Shimada, I. / Arata, Y.
#2: Journal: Biochemistry / Year: 1992
Title: Dynamical Structure of the Antibody Combining Site as Studied by 1H-15N Shift Correlation NMR Spectroscopy
Authors: Takahashi, H. / Suzuki, E. / Ishimadaarata, Y.
#3: Journal: Biochemistry / Year: 1992
Title: Isotope-Edited Nuclear Magnetic Resonance Study of Fv Fragment of an Anti- Dansyl Mouse Monoclonal Antibody: Recognition of the Dansyl Hapten
Authors: Odaka, A. / Kim, J.I. / Takahashi, H. / Shimada, I. / Arata, Y.
#4: Journal: Biochemistry / Year: 1991
Title: Preparation of the Fv Fragment from a Short-Chain Mouse IgG2a Anti-Dansyl Monoclonal Antibody and Use of Selectively Deuterated Fv Analogues for Two- Dimensional 1H NMR Analyses of Antigen-Antibody Interactions
Authors: Takahashi, H. / Igarashi, T. / Shimada, I. / Arata, Y.
#5: Journal: Biochemistry / Year: 1991
Title: Multinuclear NMR Study of the Structure of the Fv Fragment of Anti-Dansyl Mouse IgG2a Antibody
Authors: Takahashi, H. / Odaka, A. / Kawaminami, S. / Matsunaga, C. / Kato, K. / Shimada, I. / Arata, Y.
#6: Journal: J.Am.Chem.Soc. / Year: 1991
Title: Conformation and Stereoselective Reduction of Hapten Side Chain in the Antibody Combining Site
Authors: Kimnakano, T. / Higuchi, T. / Hirobe, M. / Shimada, I. / Arata, Y.
#7: Journal: Biochemistry / Year: 1990
Title: Structure of a Mouse Immunoglobulin G that Lacks the Entire CH1 Domain: Protein Sequencing and Small-Angle X-Ray Scattering Studies
Authors: Igarashi, T. / Sato, M. / Katsube, Y. / Takio, K. / Tanaka, T. / Nakanishi, M. / Arata, Y.
History
DepositionDec 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 17, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)-KAPPA (LIGHT CHAIN))
H: PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7324
Polymers26,5402
Non-polymers1922
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.290, 66.930, 53.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)-KAPPA (LIGHT CHAIN))


Mass: 12386.949 Da / Num. of mol.: 1
Fragment: FV FRAGMENT (VL DOMAIN) SYNONYM: ANTI-DANSYL FV FRAGMENT
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / References: UniProt: P01631
#2: Antibody PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) (HEAVY CHAIN))


Mass: 14152.787 Da / Num. of mol.: 1
Fragment: FV FRAGMENT (VH DOMAIN) SYNONYM: ANTI-DANSYL FV FRAGMENT
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / References: UniProt: P01801
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPAOUND THE FV FRAGMENT WAS PROPARED BY A PROTEOLYTIC DIGESTION OF ANTI-DANSYL MONOCLONAL ...COMPAOUND THE FV FRAGMENT WAS PROPARED BY A PROTEOLYTIC DIGESTION OF ANTI-DANSYL MONOCLONAL ANTIBODY. THE FV FRAGMENT WAS COMPOSE OF 237 AMINO ACID RESIDUES (113 RESIDUES IN THE VL DOMAIN AN 124 RESIDUES IN THE VH DOMAIN). THE FV FRAGMENT WAS PREPARED BY A PROTEOLYTIC DIGESTION OF ANTI-DANSYL MONOCLONAL ANTIBODY. THE FV FRAGMENT IS COMPOSED OF 237 AMINO ACID RESIDUES (113 RESIDUES IN THE VL DOMAIN AND 124 RESIDUES IN THE VH DOMAIN).
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.7 % / Description: DATA WERE COLLECTED BY OSCILLATION METHOD
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.75
Details: CRYSTALLIZATION CONDITIONS: TEMPERATURE AT 20C. PRECIPITANT SOLUTION CONTAINED 1 AMMONIUM SULFATE AND 0.025 M SODIUM CACODYLATE (PH 6.75). 5 MG/ML OF FV FRAGMENT., VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.8 Mammonium sulfate1drop
325 mMsodium cacodylate1drop
41.6 Mammonium sulfate1reservoir
525 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 10, 1998 / Details: DOUBLE FOCUSING MIRROR (PT COATED AND NI COATED)
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 32405 / % possible obs: 97.6 % / Observed criterion σ(I): 1 / Redundancy: 11.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 42.6
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.5 / % possible all: 93
Reflection
*PLUS
Highest resolution: 1.55 Å / Num. obs: 29973 / % possible obs: 97.7 % / Num. measured all: 331744 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.57 Å / % possible obs: 96.3 % / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGF

1igf


Resolution: 1.55→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000 / Data cutoff low absF: 1 / Isotropic thermal model: GAUSS / Cross valid method: THROUGHOUT / σ(F): 2 / Details: ALL ATOMS IN THE ASYMMETRIC UNIT WERE REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3216 10 %RANDOM
Rwork0.184 ---
obs0.184 32150 96.8 %-
Displacement parametersBiso mean: 13.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.55→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 10 400 2282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.022
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.584
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.55→1.57 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.33 83 11.4 %
Rwork0.34 780 -
obs--96.9 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 28800 / Rfactor obs: 0.179 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.584

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